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The Portland & Western's roots are in sister company Willamette and Pacific Railroad, founded in 1993. This company was created to take over operations on many branchlines of the Southern Pacific, a Class I railroad. These branches included the Toledo Branch from Albany to Toledo and the Westside Branch from Monroe to St. Joseph (near McMinnville), plus the Bailey Branch west from Monroe to a sawmill, the Dallas Branch from Gerlinger to Dallas, the Willamina Branch from Whiteson (near Amity) to Willamina, and the southern portion of the Newberg Branch from St. Joseph to Springbrook (north of Newberg). Lumber products and paper are the predominate commodity on these branches, along with some agricultural products from various shippers. The Cascade Steel Rolling Mill in McMinnville is an important shipper as well, and propane shipments are handled to several distributors.

PNWR was created in 1995 to take over operations of the remainder of the SP's branchlines in the state consisting of the former Southern Pacific Tillamook Branch between Willsburg Junction (near Milwaukie) and Hillsboro, the Westside-Seghers Branch from Hillsboro to Seghers (near Gaston), and the remaining segment of the Newberg Branch between Cook (near Tualatin) and Springbrook (near Newberg), connecting to the existing Willamette & Pacific network to McMinnville and Corvallis. The W&P had trackage rights on the Newberg Branch and the portion of the Tillamook Branch between Cook and Willsburg Junction, along with trackage rights on a short portion of SP's mainline to Brooklyn Yard to facilitate interchange with SP, however in the year prior to the P&W's formation the W&P had been interchanging with SP exclusively through the Eugene Yard gateway.

According to former WPRR/PNWR General Manager Robert I. Melbo, the Portland & Western was created to take over the new lines, rather than just extending the WPRR, due to regulatory issues then in force.

Most of the former SP branches are operated via a twenty year lease agreement, which in the wake of the 1996 Union Pacific-Southern Pacific merger, are now held by UP. The operations on the former BN branches are mixed between leases and outright ownership.

Originally, the Portland & Western has been operated as a "paper corporation". Its officers were the same as those of the sister WPRR, with which its lines are contiguous. WPRR locomotives and other equipment were used to operate the line, and all locomotives are painted and/or lettered for the PNWR as a publicity move. Operating crews were divided between the two companies, but in practice, crews of PNWR or WPRR would be used anywhere they were needed on the system.

The late 1990s brought changes to the relationship. System additions which brought with them more operations in Portland led the company to move its headquarters north from Albany to Salem, Oregon. With an increasing profile in the metro area, the Portland & Western became the predominant corporate image in December 2000. Everything from locomotives to letterheads began to bear the brand Portland & Western. In effect, the situation of 1995 has been reversed, and WPRR is now the paper corporation.

The combined PNWR/WPRR system has expanded rapidly. In 1997, PNWR acquired the "Astoria Line", running from Northwest Portland through to the deepwater Port of Astoria from Burlington Northern. At nearly 92 miles in length, the line brought a significant number of paper, lumber, and chemical customers onto the system. In 2002, PNWR acquired a long term lease of the remaining Burlington Northern branches in the state, giving the company access to Salem and Eugene via its own tracks. The acquisition of the former allowed PNWR to make through movements from its Portland area lines to its central yard at Albany without routing over the steep and curvy Rex Hill.

Three other shortlines which interchange with PNWR are of note. The first is the Port of Tillamook Bay Railroad,[1] which interchanges with PNWR solely. This line carries a significant number of carloads, primarily lumber, from Tillamook, Oregon, over the coast range via 100 miles of winding mountain railway. The POTB line was severely damaged by a major storm in 2007, and is out of service indefinitely, west of Banks.[2][3]

The second is the Albany and Eastern Railroad a subsidiary of the Rick Franklin Corp, which interchanges solely with the PNWR. This shortline is in part the Southern Pacific line to Detroit, Oregon as well as the Spokane, Portland and Seattle Ry's line to Sweet Home, Oregon. This line carries lumber and scrap steel. The Rick Franklin Corp also operates a railroad maintenance service that is based out of Lebanon, Oregon.

The third is the Central Oregon and Pacific Railroad, a subsidiary of GWI. Although CORP and PNWR cross each other in Eugene, Oregon, operating agreements with Union Pacific prevented the two railroads from interchanging traffic directly. Congestion problems experienced by UP in 2004 resulted in a new agreement allowing direct interchange, creating a new traffic flow on PNWR. Today, PNWR handles a great deal of log traffic from a log import-export firm on its lines in Rainier, Oregon, clear across the entire system to an interchange with CORP at Eugene.

PNWR operates between 20 and 30 trains per day over its system. PNWR's main yard, shops complex, and dispatcher are all located at Albany. Additional crew bases in St. Helens, Tigard, McMinnville, and Eugene. Executive offices are maintained in Salem. As of November 29, 2008 P&W is operating with an interim President and General Manager. A. Bruce Carswell resigned from the post in November 2008, replacing Larry Phipps, who retired in November 2005, who had replaced Robert I. Melbo who was WPRR/PNWR's first President and General Manager, having previously been the Superintendent of the Southern Pacific's Oregon Division which operated many of the lines before the WPRR was formed.

Primary trains on the system are the "Harbor Turn/Albany Turn" pair, which runs from Portland through to Albany; the "Toledo Hauler", running from Albany over the Coast Range to Toledo; the "Eugene Hauler", from Albany to a Eugene interchange with UP over UP trackage rights; the "Westsider" running from Albany to McMinnville; and the Albany Hauler from Albany to a CORP interchange at Eugene, via the PNWR's leased BN trackage. In 2006, PNWR took over operation of the 663/664 train pair from BNSF Railway. These trains run between Vancouver, WA and Albany (663 is the southbound train, 664 goes north) and are PNWR's first to regularly operate outside of Oregon. They alternately use the Oregon Electric District out of Portland and a nearby Union Pacific line between Portland and Salem under an inherited trackage rights agreement. As of September 2008, PNWR was operating run-through unit[clarification needed] grain trains from the BNSF to and from Port Westward on the Astoria Line west of Rainier.[citation needed] These trains currently run with BNSF locomotives.[citation needed]

Two standard-fare Portland and Western locomotives in Beaverton, Oregon.

The locomotive fleet of the PNWR/WPRR primarily consists of used "second generation" products of General Motors' Electro-Motive Division. Notable exceptions in the fleet include a handful of GP/SD/SW9 locomotives which are now 50 years old and still in regular service. PNWR also operates a few unique locomotives, an SD40-3MR, PNWR 3300, as well as one of the last remaining SDP40Fs, DLMX 644.

Most of the company's rolling stock is marked for WPRR, but some stock carries the PNWR mark. There are a number of WPRR woodchip gondolas for woodchip service and centerbeam flatcars for lumber. Three of the railroad's woodchip cars have special paint schemes. One is in green and yellow to honor the University of Oregon, and includes the school's "duck" logo. Another is in orange and black, honoring Oregon State University, and includes that school's "beaver" emblem. And the third is painted black with the red "DARE" logo to promote the Drug Abuse Resistance Education program. In 2007, WPRR added 200 log flats that were purchased from BCOL, and are now marked WPRR 62001 through 62200.

In late 2008, some of the WPRR woodchip gondola fleet leases expired and the reporting marks changed from WPRR to AOK on cars 74503 to 74510. Also, due to the economic contraction in the U.S., virtually all of the WPRR centerbeam fleet has returned to the railroad for long-term storage. The centerbeam cars are stored primarily on the Bailey District, south of Corvallis, Oregon, and at the old Valley & Siletz Railway yard, north of Independence, Oregon.

The PNWR line between Beaverton and Wilsonville is leased to TriMet for operation of its Westside Express Service (WES) commuter rail service.[4] PNWR freight trains also continue to use the line, but not during times when the passenger trains are operating.[5] Under a contract with TriMet,[5] the rail cars are operated by PNWR crews.

Begun in the 1990s and originally led by Washington County, the commuter-rail project was taken over by TriMet in 2002,[6] and the regional transit agency entered into an agreement with PNWR for the use of its right-of-way, and later for the operation of the rail cars. During construction in 2007–2008, the section involved was upgraded for use by commuter trains. Upgrades included a new roadbed, ballast, ties and rail to accommodate passenger train speeds of 60 MPH and freight train speeds of 40 MPH, Centralized Traffic Control signaling, Automatic Train Stop at control points, new sidings, station platforms at the end points along with intermediate stations in Tigard, Oregon and Tualatin, Oregon, and in the Progress/Washington Square area near the Beaverton/Tigard city line, and a maintenance shop located in Wilsonville (staffed by TriMet employees). In Beaverton, TriMet also constructed a new 1,700-foot (520 m) spur off of the PNWR line, for exclusive use by WES trains, running mostly along Lombard Avenue and connecting the freight line with the Beaverton Transit Center.[7]

PNWR is responsible for train operations, including staffing the trains with an engineer and conductor, dispatching, and maintenance. TriMet has a manager to oversee the service and handles basic maintenance of the fleet and stations.

The service had been expected to launch as early as August 2008 but due to delays by the car manufacturer, Colorado Railcar, the actual start of service date was February 2, 2009. Four Colorado Railcar DMUs are used, three of which are powered vehicles and can move on their own, and a fourth vehicle which is a control trailer that is towed or pushed by one of the three powered cars. The vehicles are of the Aero DMU design featuring a styled cab at one end; the three powered cars also have a flat cab on the opposite end. Since the trains operate in both directions without turning the vehicle around at the end of the route, the powered cars running as single units operate "backwards" much of the time. The vehicles are equipped with two doors per vehicle side, plush leather seats, four bicycle racks, air conditioning, and free wireless internet access. The vehicles are owned by TriMet and are painted in TriMet's scheme similar to its buses and MAX light rail vehicles. TriMet also acquired two former Alaska RailroadRail Diesel Cars, or RDCs, in late 2009 and refurbished them to serve as a backup train on occasions when one or more of the DMUs are out of service.

Fares are handled off-board using ticket-vending machines at each stop, which will not allow for cash fares but only the use of a credit or debit card. Cash passengers have the option in Tigard and Beaverton to first board a bus at the transit center to pay for cash and obtain a transfer which will be valid on the train; in Tualatin, Hall/Nimbus bus service is infrequent to accommodate this, and TriMet does not serve Wilsonville and thus a passenger in Wilsonville wanting to pay a cash fare will simply not be permitted to board.